XB-FEAT-6467139

ces2/ces2.1

This is the community wiki page for the gene ces2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature changes

On December 28, 2018, this gene was changed from ces3 to ces3.1. Evidence includes the Ensembl CES3 gene tree as well as partial synteny with human CES3 locus.

05JUNE 2023

Xenopus gene changed from ces3.1 to ces3.

18SEPT2023

Xenopus gene symbol and gene name changed from ces3.1, carboxylesterase 3, gene 1 to ces2.1, carboxylesterase 2, gene 1 following phylogenetic analysis, synteny analysis and by applying Xenopus nomenclature rules to this gene expansion on chromosome 4.

The Xenopus genes are duplicates within a single clade, which is most closely relates to the Human CES2 genes, not the CES3 genes as previously thought.

Applying Xenopus nomenclature, we have renamed all CES2 orthologs , with X. tropicalis ces2.1-ces2.8, from left to right, and X. laevis' genes ces2.1.L-ces2.5.L from left to right. There are no genes on the X. laevis S subgenome.

synteny and orthology

18SEPT2023

There are 5 x ces# genes in X. laevis on Chr4L and 8 x ces# genes in X. tropicalis on chromosome 4, flanked by wtip and uba2 downstream, and ankar-like, rrad, and cdh16 upstream. There are no ces2 paralogs in the v10 annotation X. laevis S sub genome

Here the order of genes are compared with across species, with new ces2 gene assignment in bold. Note that Human has 3 CES genes, all likely a result of a duplication event, and the goal was to determine which of these genes is the closest ortholog to the frog gene-expansion.

Xtrop chr4: wtip< uba2< (GeneID: 100144981)ces3.1>ces2.1 LOC100493994(ces2-like)>ces2.2 (GeneID:394897)ces5A> ces2.3 (GeneID:779633)ces3.4>ces2.4 LOC116410405>ces2.5 (GeneID:100493652)ces3.5>ces2.6 LOC100493819>ces2.7 (GeneID:100494149)ces3.7>ces2.8 LOC105945786(ankar-like)< rrad> cdh16>

Xlaevis chr4L: wtip.L< uba2.L< LOC108714107(ces5a)>ces2.1.L (GeneID:100381172)ces3.4.L>ces2.2 LOC108713509>ces2.3 LOC108714105(ces5a-like)>ces2.4 LOC108713647(cesE2)>ces2.5 LOC121403150(ankar-like) rrad.L

X.laevis chr4S: wtip.S< uba2.S> rrad.S> pdp2.S ca7.S cyba.S

H.sapiens Chr6: B3GNT9 PHAF1 CBFB RN7SL543P CES4A CES3 LOC107984881(ncRNA) CES2 CIAO2B RRAD CDH16

protein alignment and phylogenetic anayslis

18SEPT2023

An alignment and cladogram of all isoforms of the Xenopus ces# proteins was run against all isoforms of the 3 Human CES genes (CES2 CES3 and CES4A, which are all adjacent to each other on CHR6). The results strongly support the hypothesis that the Xenopus clade most closely related to the human CES2 gene, not CES3 (or CES4A) as previously thought.

All Xenopus genes cluster with each other, and not any of the human genes.

proteins accession used in this analysis: NP_001120019.1 XP_004913616.1 NP_001265277.1 NP_001072187.1 XP_031756663.1 XP_031756661.1 XP_002935836.3 XP_002943465.3 XP_018113499.1 XP_018113497.1 XP_018112562.1 XP_041446147.1 XP_041446153.1 NP_001352334.1 NP_001172105.1 NP_001177130.1 XP_031756662.1 XP_004913614.2 XP_041446148.1 NP_001352335.1 NP_001172106.1 NP_001177131.1 XP_031756660.1 XP_041446149.1 NP_001352336.1 NP_079198.2 NP_001305435.1

Furthermore, note that human CES5A does not have any amphibian orthologs recognized by NCBI, and it does not share a conserved syntenic position(s) with Xenopus. Furthermore EBI's EggNogg gene/protein family/homology tree for CES5A indictates that CES5A is a mammal specific gene, thus frog genes should NOT be called ces5A , although several were annotated as ces5a in the v10 genome annotations.

Human CES5A (Gene ID: 221223 ) and mouse Ces5a (geneId: 67935) have been removed from all of these Xenopus ces2gene pages.